Plant roots generally account for over 50% of a plant's biomass. Part of that biomass includes the root microbiome, which is the assemblage of bacteria and fungi living in the rhizosphere (typically the 1-3 mm region adjacent to the external surface of the root). Soil bacteria that associate with plant roots and have a positive effect on plant growth are generally known as plant growth-promoting bacteria (PGPBs). PGPBs can fix nitrogen, secrete plant hormones or antibiotics, solubilize phosphate, inhibit pathogenic microorganisms, and/or modify insoluble Fe3+ to utilizable forms of iron (Lugtenberg & Kamilova, 2009; and Ortíz-Castro et al., 2009). In addition, soil bacteria can also stimulate phytoremediation and by attaching to roots, and improve plant health by increasing the numbers of biodegradative bacteria (Glick, 2010).
Many PGPB studies have focused on Gram-negative bacteria such as the pseudomonads, which are simple to culture and suitable for genetic manipulation. However, a large number of additional microorganisms also exhibit plant growth-promoting (PGP) activity. For example, several Bacillus species have been shown to have PGP activity (Zhang J. et al., 1996; Zhang H. et al., 2008; Zhang H. et al., 2010; Idris et al., 2007; Benhamou et al., 1996; Probanza et al., 2001; Bai et al., 2003; Handelsman et al., 1990; and López-Bucio et al., 2007). Combinations of several Bacillus species have also been shown to enhance plant growth. For example, Francis et al. (2010) describe the interactions of Bacillus species as well as other Gram-positive bacteria with plants. It has also been shown that co-inoculating legumes with rhizobia and various Bacillus species, including B. subtilis, resulted in altered root architecture and enhanced nodulation for bean (Petersen et al., 1996; and Srinivasan et al., 1997), peanut (Turner & Backman, 1991), pigeon pea (Rajendran et al., 2008), and soybean (Halverson & Handelsman, 1991; and Bai et al., 2003). Accordingly, even within a well-studied genus like Bacillus, a need exits for identifying and isolating additional new microorganisms with PGP activity.
It has also been shown that microorganism diversity and complexity on the surfaces of plant roots are highly correlated with edaphic factors such as moisture, pH, climate, parent rock material, temperature, and nutrient and organic matter content (Lau and Lennon, 2011; and Brockett et al., 2012). However, the plants themselves also have a significant influence on the composition of their microbiomes, especially in the rhizosphere. Plants that live in harsh environments (e.g., arid and nutrient-poor environments), such as deserts, have been called “resource” (Halvorson et al., 1994) or “fertility” islands (Schlesinger et al., 1996) because they support a diversity of organisms within and below their root system in spite of the challenging conditions of desiccation and low nutrient availability. Plants adapted to harsh environments and their association with microorganisms within these habitats makes both partners highly competitive and adaptive (Basil et al., 2004).
The majority of studies on microbial communities have been limited to those from mesic environments (e.g., forests, grasslands, and agricultural fields), whereas very few studies have been performed on desert or other arid environment root microbiomes (Barns et al., 1999). However, those few studies of microbial communities within various desert environments have revealed both antifungal (Basil et al., 2004) and antibiotic (Hozzein et al., 2008) properties, indicating that desert habitats may be a source of plant growth-promoting microorganisms. With increasing demands for food as the world's human population expands, more and more desert land is being utilized for either food or biofuel crop production. Thus, there also exists a need for identifying and isolating additional microorganisms from harsh environments, such as deserts, that promote plant growth of crop plants cultivated in such harsh environments.